ABSTRACT Many of the molecular mechanisms underlying well-characterized robust and rapidly inducible transcriptional responses are shared among other systems, so we use the transcriptional response to estrogen treatment as a model to study gene regulation. We use rapid kinetic regulation and perturbation of transcription cascades, transcription factors, and cofactors to identify key mechanisms, genes, and regulatory elements that are critical for estrogen signaling. Transcription factors act as activators or repressors and interface with a constellation of accessory cofactors to regulate distinct steps in the transcription to coordinate gene expression, but the molecular functions of the vast majority of transcription factors remain uncharacterized. We will use molecular genomics and computational methods to classify transcription factors by their molecular function, as opposed to broad activator and repressor classes, in order to understand the context specificity of gene regulation. We recently found that the estrogen receptor transcription factor may compete with other transcription factors for limiting cofactors to mediate estrogen-induced repression. We will develop light inducible dominant negative peptide inhibitors to test various models of repression and address the challenges of studying estrogen- repressed genes. The genes and regulatory elements that are downstream of the first wave of transcriptional response are critical for propagating regulatory cascades. We will generate high temporal resolution time course data and implement statistical modeling approaches to identify effector genes and regulatory elements that are critical for estrogen signaling. Our research will continue to reveal basic principles and rules that govern transcription factor specificity in order to someday understand how genetics, nutrition, and environmental factors contribute to variation in transcriptional programs that can lead to disease states or ineffective therapies.